The mission of DMASoftware Inc. is to enable the field of genomics by writing enterprise grade simulation software that incorporates state-of-the-art knowledge of the thermodynamics and kinetics of nucleic acid folding and hybridization. To accomplish this goal, DNA Software has built the Oligonucleotide Modeling Platform (OMP), which accurately predicts target secondary structure, calculates probe hybridization thermodynamics, simulates DNA or RNA based assays, automatically selects probes and PCR primers, and integrates BLAST and CLUSTAL sequence alignment capabilities. OMP uses a standardized architecture, which allows it to accept deferent input and output data structures and to combine modules in a deployable fashion. OMP has been successfully commercialized and shown to reduce the development time and improve the reliability of any process involving Oligonucleotide hybridization such as multiplex PCR, DNA sequencing, SNP detection assays, mRNA expression profiling, and a variety of chip arrays. This proposal focuses on the expansion of OMP capability to design probes and primers that contain modified nucleotides, fluorophore labels and hybridize in the presence of buffer additives. This will enable nucleic acid based diagnostic applications that utilize these modifications to enhance sensitivity, specificity, multiplexing and to improve in vivo properties of diagnostic probes. At present, the lack of experimental thermodynamic parameters for modified nucleotides, fluorophores and buffer additives impairs OMP accuracy in predicting hybridization and designing efficient modified oligonucleotides. This proposal will close this gap by providing experimentally measured thermodynamic parameters for most commonly used modifications, fluorophores and buffer additives. These parameters will be incorporated into OMP as well as made publicly available.